From 9eb1f5aebeb7ce215a658ba12ca5255a27af50d1 Mon Sep 17 00:00:00 2001
From: Winston Olson-Duvall <winston.olson-duvall@jpl.nasa.gov>
Date: Tue, 1 Mar 2022 14:45:10 -0800
Subject: [PATCH 01/13] Add algo config, imgspec run file and supporting script
 for registering an imgspec algorithm.

---
 .imgspec/algorithm_config.yaml      | 25 +++++++++++++
 .imgspec/get_paths_from_granules.py | 56 +++++++++++++++++++++++++++++
 .imgspec/imgspec_run.sh             | 50 ++++++++++++++++++++++++++
 3 files changed, 131 insertions(+)
 create mode 100644 .imgspec/algorithm_config.yaml
 create mode 100644 .imgspec/get_paths_from_granules.py
 create mode 100644 .imgspec/imgspec_run.sh

diff --git a/.imgspec/algorithm_config.yaml b/.imgspec/algorithm_config.yaml
new file mode 100644
index 0000000..054eb58
--- /dev/null
+++ b/.imgspec/algorithm_config.yaml
@@ -0,0 +1,25 @@
+# DO NOT DELETE
+# THIS CONFIG IS AUTO-GENERATED BY ADE UI
+algo_name: SpectralUnmixing
+version: imgspec
+environment: ubuntu
+repository_url: https://github.com/emit-sds/SpectralUnmixing.git
+docker_url: registry.imgspec.org/root/ade_base_images/spectral-unmixing:latest
+
+# fill out these fields
+# explain what this algorithm does
+description: A general, fast, and flexible package for spectral unmixing.
+# path to the wrapper script for running the algorithm
+run_command: SpectralUnmixing/.imgspec/imgspec_run.sh
+# set a storage value in GB or MB or KB, e.g. "100GB", "20MB", "10KB"
+disk_space: 80GB
+inputs:
+# remove below this line if no inputs
+# rename and set algorithm input names accordingly
+  - name: reflectance_granule
+    type: file
+  - name: endmember_library
+    type: positional
+  - name: endmember_column
+    type: positional
+    default: "class"
diff --git a/.imgspec/get_paths_from_granules.py b/.imgspec/get_paths_from_granules.py
new file mode 100644
index 0000000..b712731
--- /dev/null
+++ b/.imgspec/get_paths_from_granules.py
@@ -0,0 +1,56 @@
+#! /usr/bin/python
+
+import argparse
+import glob
+import os
+import sys
+import tarfile
+
+
+def parse_args():
+    parser = argparse.ArgumentParser()
+    products = ["rfl"]
+    formats = ["envi"]
+    parser.add_argument("-p", "--product",
+                        help=("Choose one of the following product types: " + ", ".join(products)))
+    parser.add_argument("-f", "--format",
+                        help=("Choose one of the following formats: " + ", ".join(formats)))
+    args = parser.parse_args()
+
+    if args.product:
+        if args.product not in products:
+            print("ERROR: Product \"%s\" is not a valid product choice." % args.product)
+            sys.exit(1)
+    if args.format:
+        if args.format not in formats:
+            print("ERROR: Format \"%s\" is not a valid format choice." % args.format)
+            sys.exit(1)
+    return args
+
+
+def main():
+    args = parse_args()
+
+    # Unzip and untar granules
+    input_dir = "input"
+    granule_paths = glob.glob(os.path.join(input_dir, "*.tar.gz"))
+    for g in granule_paths:
+        tar_file = tarfile.open(g)
+        tar_file.extractall(input_dir)
+        tar_file.close()
+        os.remove(g)
+
+    # Get paths based on product type file matching
+    paths = []
+    if args.product == "rfl":
+        # AVIRIS SDS uses *rfl*img and *corr*img for distributed files
+        paths = glob.glob(os.path.join(input_dir, "*", "*rfl*img"))
+        paths += glob.glob(os.path.join(input_dir, "*", "*corr*img"))
+        # ISOFIT uses *rfl for processed reflectance files
+        paths += glob.glob(os.path.join(input_dir, "*", "*rfl"))
+
+    print(",".join(paths))
+
+
+if __name__ == "__main__":
+    main()
diff --git a/.imgspec/imgspec_run.sh b/.imgspec/imgspec_run.sh
new file mode 100644
index 0000000..3457299
--- /dev/null
+++ b/.imgspec/imgspec_run.sh
@@ -0,0 +1,50 @@
+#!/bin/bash
+
+# Description:
+#
+# The top-level run script to execute unmix.jl on ImgSPEC. This script accepts the inputs described in the
+# algorithm_config.yaml file and pre-processes them as needed to pass into SpectralUnmixing/unmix.jl.  This script
+# is currently compatible with AVIRIS Classic, AVIRIS-NG, and PRISMA data.
+#
+# Inputs:
+#
+# $1: URL of endmember library
+# $2: Column name from endmember library that describes the library classes (default is "class")
+#
+# In addition to the positional arguments, this script expects a downloaded reflectance granule to be present in a
+# folder called "input".
+
+
+imgspec_dir=$( cd "$(dirname "$0")" ; pwd -P )
+specun_dir=$(dirname ${imgspec_dir})
+
+input="input"
+mkdir -p output
+
+# Spectral Unmixing paths
+unmix_exe="$specun_dir/unmix.jl"
+endmember_library_path="$input/endmember_library.csv"
+
+# Get reflectance path from input granule
+echo "Looking for input granule gzip and extracting to get reflectance path..."
+rfl_path=$(python ${imgspec_dir}/get_paths_from_granules.py -p rfl)
+echo "Found input reflectance file: $rfl_path"
+
+# Process positional args to get EcoSIS CSV files
+echo "Getting endmember library..."
+curl --retry 10 --output $endmember_library_path $1
+
+# Get output base from reflectance path
+rfl_name=$(basename $rfl_path)
+output_base="output"
+if [[ rfl_name == f* ]]; then
+    output_base=$(echo rfl_name | cut -c1-16)
+elif [[ rfl_name == ang* ]]; then
+    output_base=$(echo rfl_name | cut -c1-18)
+elif [[ rfl_name == PRS* ]]; then
+    output_base=$(echo rfl_name | cut -c1-38)
+fi
+
+cmd="julia $unmix_exe $rfl_path $endmember_library_path $2 $output_base"
+echo "Executing command: $cmd"
+$cmd

From a064f99e51de60d91a5056f2ae34436f34e5ab62 Mon Sep 17 00:00:00 2001
From: Winston Olson-Duvall <winston.olson-duvall@jpl.nasa.gov>
Date: Tue, 1 Mar 2022 15:49:09 -0800
Subject: [PATCH 02/13] Install Julia deps before running command.

---
 .imgspec/imgspec_run.sh | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.imgspec/imgspec_run.sh b/.imgspec/imgspec_run.sh
index 3457299..fd202ee 100644
--- a/.imgspec/imgspec_run.sh
+++ b/.imgspec/imgspec_run.sh
@@ -14,7 +14,6 @@
 # In addition to the positional arguments, this script expects a downloaded reflectance granule to be present in a
 # folder called "input".
 
-
 imgspec_dir=$( cd "$(dirname "$0")" ; pwd -P )
 specun_dir=$(dirname ${imgspec_dir})
 
@@ -45,6 +44,9 @@ elif [[ rfl_name == PRS* ]]; then
     output_base=$(echo rfl_name | cut -c1-38)
 fi
 
+echo "Setting up Julia dependencies..."
+julia -e 'using Pkg; Pkg.activate("."); Pkg.add(path="https://github.com/kmsquire/ArgParse2.jl"); Pkg.instantiate()'
+
 cmd="julia $unmix_exe $rfl_path $endmember_library_path $2 $output_base"
 echo "Executing command: $cmd"
 $cmd

From c16d0081a3ed8ed4c129d0b5345853249b4dfc66 Mon Sep 17 00:00:00 2001
From: Winston Olson-Duvall <winston.olson-duvall@jpl.nasa.gov>
Date: Tue, 1 Mar 2022 15:51:08 -0800
Subject: [PATCH 03/13] Make imgspec_run.sh executable.

---
 .imgspec/imgspec_run.sh | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 mode change 100644 => 100755 .imgspec/imgspec_run.sh

diff --git a/.imgspec/imgspec_run.sh b/.imgspec/imgspec_run.sh
old mode 100644
new mode 100755

From 267b235d5728adaa416c3ad5686a86764ee9e18b Mon Sep 17 00:00:00 2001
From: Winston Olson-Duvall <winston.olson-duvall@jpl.nasa.gov>
Date: Tue, 1 Mar 2022 16:10:58 -0800
Subject: [PATCH 04/13] Fix output base path - this version works when running
 in ADE.

---
 .imgspec/imgspec_run.sh | 30 +++++++++++++++++++-----------
 1 file changed, 19 insertions(+), 11 deletions(-)

diff --git a/.imgspec/imgspec_run.sh b/.imgspec/imgspec_run.sh
index fd202ee..54984e9 100755
--- a/.imgspec/imgspec_run.sh
+++ b/.imgspec/imgspec_run.sh
@@ -14,12 +14,20 @@
 # In addition to the positional arguments, this script expects a downloaded reflectance granule to be present in a
 # folder called "input".
 
+# Define some useful directories
 imgspec_dir=$( cd "$(dirname "$0")" ; pwd -P )
 specun_dir=$(dirname ${imgspec_dir})
-
+cur_dir=$(pwd -P)
 input="input"
 mkdir -p output
 
+# Set up Julia dependencies and project
+echo "Setting up Julia dependencies..."
+cd $specun_dir
+julia -e 'using Pkg; Pkg.activate("."); Pkg.add(path="https://github.com/kmsquire/ArgParse2.jl"); Pkg.instantiate()'
+export JULIA_PROJECT=$specun_dir
+cd $cur_dir
+
 # Spectral Unmixing paths
 unmix_exe="$specun_dir/unmix.jl"
 endmember_library_path="$input/endmember_library.csv"
@@ -36,17 +44,17 @@ curl --retry 10 --output $endmember_library_path $1
 # Get output base from reflectance path
 rfl_name=$(basename $rfl_path)
 output_base="output"
-if [[ rfl_name == f* ]]; then
-    output_base=$(echo rfl_name | cut -c1-16)
-elif [[ rfl_name == ang* ]]; then
-    output_base=$(echo rfl_name | cut -c1-18)
-elif [[ rfl_name == PRS* ]]; then
-    output_base=$(echo rfl_name | cut -c1-38)
+if [[ $rfl_name == f* ]]; then
+    output_base=$(echo $rfl_name | cut -c1-16)
+elif [[ $rfl_name == ang* ]]; then
+    output_base=$(echo $rfl_name | cut -c1-18)
+elif [[ $rfl_name == PRS* ]]; then
+    output_base=$(echo $rfl_name | cut -c1-38)
 fi
+output_base_path="output/$output_base"
+echo "Output base path: $output_base_path"
 
-echo "Setting up Julia dependencies..."
-julia -e 'using Pkg; Pkg.activate("."); Pkg.add(path="https://github.com/kmsquire/ArgParse2.jl"); Pkg.instantiate()'
-
-cmd="julia $unmix_exe $rfl_path $endmember_library_path $2 $output_base"
+# Build command and execute
+cmd="julia $unmix_exe $rfl_path $endmember_library_path $2 $output_base_path"
 echo "Executing command: $cmd"
 $cmd

From 34787e67623b7d1b27c882a40247beeef208c8a0 Mon Sep 17 00:00:00 2001
From: Winston Olson-Duvall <winston.olson-duvall@jpl.nasa.gov>
Date: Wed, 2 Mar 2022 15:16:33 -0800
Subject: [PATCH 05/13] Add JULIA_DEPOT_PATH and some logging to debug.

---
 .imgspec/imgspec_run.sh | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.imgspec/imgspec_run.sh b/.imgspec/imgspec_run.sh
index 54984e9..b0e4792 100755
--- a/.imgspec/imgspec_run.sh
+++ b/.imgspec/imgspec_run.sh
@@ -24,6 +24,9 @@ mkdir -p output
 # Set up Julia dependencies and project
 echo "Setting up Julia dependencies..."
 cd $specun_dir
+echo "JULIA_DEPOT_PATH before: $JULIA_DEPOT_PATH"
+export JULIA_DEPOT_PATH=/app/.julia
+echo "JULIA_DEPOT_PATH after: $JULIA_DEPOT_PATH"
 julia -e 'using Pkg; Pkg.activate("."); Pkg.add(path="https://github.com/kmsquire/ArgParse2.jl"); Pkg.instantiate()'
 export JULIA_PROJECT=$specun_dir
 cd $cur_dir

From 8ea8f3a0dada4e6af941a918264de6db1420f20c Mon Sep 17 00:00:00 2001
From: Winston Olson-Duvall <winston.olson-duvall@jpl.nasa.gov>
Date: Thu, 3 Mar 2022 10:03:10 -0800
Subject: [PATCH 06/13] Use vanilla base image for Docker and execute all Julia
 installation steps in run script.

---
 .imgspec/algorithm_config.yaml | 2 +-
 .imgspec/imgspec_run.sh        | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.imgspec/algorithm_config.yaml b/.imgspec/algorithm_config.yaml
index 054eb58..e695e45 100644
--- a/.imgspec/algorithm_config.yaml
+++ b/.imgspec/algorithm_config.yaml
@@ -4,7 +4,7 @@ algo_name: SpectralUnmixing
 version: imgspec
 environment: ubuntu
 repository_url: https://github.com/emit-sds/SpectralUnmixing.git
-docker_url: registry.imgspec.org/root/ade_base_images/spectral-unmixing:latest
+docker_url: registry.imgspec.org/root/ade_base_images/vanilla:latest
 
 # fill out these fields
 # explain what this algorithm does
diff --git a/.imgspec/imgspec_run.sh b/.imgspec/imgspec_run.sh
index b0e4792..cf35111 100755
--- a/.imgspec/imgspec_run.sh
+++ b/.imgspec/imgspec_run.sh
@@ -23,12 +23,12 @@ mkdir -p output
 
 # Set up Julia dependencies and project
 echo "Setting up Julia dependencies..."
+conda install -c conda-forge julia=1.7
 cd $specun_dir
-echo "JULIA_DEPOT_PATH before: $JULIA_DEPOT_PATH"
-export JULIA_DEPOT_PATH=/app/.julia
-echo "JULIA_DEPOT_PATH after: $JULIA_DEPOT_PATH"
 julia -e 'using Pkg; Pkg.activate("."); Pkg.add(path="https://github.com/kmsquire/ArgParse2.jl"); Pkg.instantiate()'
 export JULIA_PROJECT=$specun_dir
+
+# Return to original directory for remainder of script
 cd $cur_dir
 
 # Spectral Unmixing paths

From 400496fc77e16e4655697551870548572b0d78fe Mon Sep 17 00:00:00 2001
From: Winston Olson-Duvall <winston.olson-duvall@jpl.nasa.gov>
Date: Fri, 4 Mar 2022 09:57:25 -0800
Subject: [PATCH 07/13] Add debugging

---
 .imgspec/algorithm_config.yaml | 2 +-
 .imgspec/imgspec_run.sh        | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/.imgspec/algorithm_config.yaml b/.imgspec/algorithm_config.yaml
index e695e45..2c48dc1 100644
--- a/.imgspec/algorithm_config.yaml
+++ b/.imgspec/algorithm_config.yaml
@@ -4,7 +4,7 @@ algo_name: SpectralUnmixing
 version: imgspec
 environment: ubuntu
 repository_url: https://github.com/emit-sds/SpectralUnmixing.git
-docker_url: registry.imgspec.org/root/ade_base_images/vanilla:latest
+docker_url: registry.imgspec.org/root/ade_base_images/plant:latest
 
 # fill out these fields
 # explain what this algorithm does
diff --git a/.imgspec/imgspec_run.sh b/.imgspec/imgspec_run.sh
index cf35111..0762bb4 100755
--- a/.imgspec/imgspec_run.sh
+++ b/.imgspec/imgspec_run.sh
@@ -23,6 +23,7 @@ mkdir -p output
 
 # Set up Julia dependencies and project
 echo "Setting up Julia dependencies..."
+echo `id`
 conda install -c conda-forge julia=1.7
 cd $specun_dir
 julia -e 'using Pkg; Pkg.activate("."); Pkg.add(path="https://github.com/kmsquire/ArgParse2.jl"); Pkg.instantiate()'

From 41e8571fb66f1eccb9efc41039d884c92a414ada Mon Sep 17 00:00:00 2001
From: Winston Olson-Duvall <winston.olson-duvall@jpl.nasa.gov>
Date: Tue, 22 Mar 2022 10:12:28 -0700
Subject: [PATCH 08/13] Add install.sh script to handle install of Julia and
 dependencies.

---
 .imgspec/algorithm_config.yaml |  4 +++-
 .imgspec/imgspec_run.sh        | 11 +----------
 .imgspec/install.sh            | 19 +++++++++++++++++++
 3 files changed, 23 insertions(+), 11 deletions(-)
 create mode 100644 .imgspec/install.sh

diff --git a/.imgspec/algorithm_config.yaml b/.imgspec/algorithm_config.yaml
index 2c48dc1..cb0aade 100644
--- a/.imgspec/algorithm_config.yaml
+++ b/.imgspec/algorithm_config.yaml
@@ -4,11 +4,13 @@ algo_name: SpectralUnmixing
 version: imgspec
 environment: ubuntu
 repository_url: https://github.com/emit-sds/SpectralUnmixing.git
-docker_url: registry.imgspec.org/root/ade_base_images/plant:latest
+docker_url: registry.imgspec.org/root/ade_base_images/vanilla:latest
 
 # fill out these fields
 # explain what this algorithm does
 description: A general, fast, and flexible package for spectral unmixing.
+# path to the build script for installing and building the algorithm in the docker image
+build_command: SpectralUnmixing/.imgspec/install.sh
 # path to the wrapper script for running the algorithm
 run_command: SpectralUnmixing/.imgspec/imgspec_run.sh
 # set a storage value in GB or MB or KB, e.g. "100GB", "20MB", "10KB"
diff --git a/.imgspec/imgspec_run.sh b/.imgspec/imgspec_run.sh
index 0762bb4..bf1482e 100755
--- a/.imgspec/imgspec_run.sh
+++ b/.imgspec/imgspec_run.sh
@@ -17,21 +17,12 @@
 # Define some useful directories
 imgspec_dir=$( cd "$(dirname "$0")" ; pwd -P )
 specun_dir=$(dirname ${imgspec_dir})
-cur_dir=$(pwd -P)
 input="input"
 mkdir -p output
 
-# Set up Julia dependencies and project
-echo "Setting up Julia dependencies..."
-echo `id`
-conda install -c conda-forge julia=1.7
-cd $specun_dir
-julia -e 'using Pkg; Pkg.activate("."); Pkg.add(path="https://github.com/kmsquire/ArgParse2.jl"); Pkg.instantiate()'
+# Export JULIA_PROJECT again in case it doesn't carry over from install.sh
 export JULIA_PROJECT=$specun_dir
 
-# Return to original directory for remainder of script
-cd $cur_dir
-
 # Spectral Unmixing paths
 unmix_exe="$specun_dir/unmix.jl"
 endmember_library_path="$input/endmember_library.csv"
diff --git a/.imgspec/install.sh b/.imgspec/install.sh
new file mode 100644
index 0000000..20b98fa
--- /dev/null
+++ b/.imgspec/install.sh
@@ -0,0 +1,19 @@
+#!/bin/bash
+
+# Install script to 1) install Julia via conda, and 2) install the Julia dependencies for this project
+
+set -x
+
+# Define some useful directories
+imgspec_dir=$( cd "$(dirname "$0")" ; pwd -P )
+specun_dir=$(dirname ${imgspec_dir})
+cur_dir=$(pwd -P)
+
+# Install Julia and then install Julia dependencies
+conda install -c conda-forge julia=1.7
+cd $specun_dir
+julia -e 'using Pkg; Pkg.activate("."); Pkg.add(path="https://github.com/kmsquire/ArgParse2.jl"); Pkg.instantiate()'
+export JULIA_PROJECT=$specun_dir
+
+# Return to original directory
+cd $cur_dir

From c1e029fe651f89b4df13e53e9e840c6dd6cb469b Mon Sep 17 00:00:00 2001
From: Winston Olson-Duvall <winston.olson-duvall@jpl.nasa.gov>
Date: Tue, 22 Mar 2022 10:13:30 -0700
Subject: [PATCH 09/13] Make install script executable.

---
 .imgspec/install.sh | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 mode change 100644 => 100755 .imgspec/install.sh

diff --git a/.imgspec/install.sh b/.imgspec/install.sh
old mode 100644
new mode 100755

From e5eada0520d0c29fa042aaef6cd9ac05c14a079a Mon Sep 17 00:00:00 2001
From: Winston Olson-Duvall <winston.olson-duvall@jpl.nasa.gov>
Date: Tue, 22 Mar 2022 15:05:31 -0700
Subject: [PATCH 10/13] Add -y flag to conda install

---
 .imgspec/install.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.imgspec/install.sh b/.imgspec/install.sh
index 20b98fa..28921bf 100755
--- a/.imgspec/install.sh
+++ b/.imgspec/install.sh
@@ -10,7 +10,7 @@ specun_dir=$(dirname ${imgspec_dir})
 cur_dir=$(pwd -P)
 
 # Install Julia and then install Julia dependencies
-conda install -c conda-forge julia=1.7
+conda install -y -c conda-forge julia=1.7
 cd $specun_dir
 julia -e 'using Pkg; Pkg.activate("."); Pkg.add(path="https://github.com/kmsquire/ArgParse2.jl"); Pkg.instantiate()'
 export JULIA_PROJECT=$specun_dir

From 821ab6fdfe24afc6c3e8a442ff2fd22a169ce329 Mon Sep 17 00:00:00 2001
From: Winston Olson-Duvall <winston.olson-duvall@jpl.nasa.gov>
Date: Wed, 23 Mar 2022 09:21:32 -0700
Subject: [PATCH 11/13] Create conda env in install script and source it in run
 script. Use vanilla 1.0 docker.

---
 .imgspec/algorithm_config.yaml |  2 +-
 .imgspec/imgspec_run.sh        |  3 +++
 .imgspec/install.sh            | 10 ++++------
 3 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/.imgspec/algorithm_config.yaml b/.imgspec/algorithm_config.yaml
index cb0aade..51bc9e7 100644
--- a/.imgspec/algorithm_config.yaml
+++ b/.imgspec/algorithm_config.yaml
@@ -4,7 +4,7 @@ algo_name: SpectralUnmixing
 version: imgspec
 environment: ubuntu
 repository_url: https://github.com/emit-sds/SpectralUnmixing.git
-docker_url: registry.imgspec.org/root/ade_base_images/vanilla:latest
+docker_url: registry.imgspec.org/root/ade_base_images/vanilla:1.0
 
 # fill out these fields
 # explain what this algorithm does
diff --git a/.imgspec/imgspec_run.sh b/.imgspec/imgspec_run.sh
index bf1482e..1230243 100755
--- a/.imgspec/imgspec_run.sh
+++ b/.imgspec/imgspec_run.sh
@@ -20,6 +20,9 @@ specun_dir=$(dirname ${imgspec_dir})
 input="input"
 mkdir -p output
 
+# Activate conda environment
+source activate spectral-unmixing
+
 # Export JULIA_PROJECT again in case it doesn't carry over from install.sh
 export JULIA_PROJECT=$specun_dir
 
diff --git a/.imgspec/install.sh b/.imgspec/install.sh
index 28921bf..9da1a1c 100755
--- a/.imgspec/install.sh
+++ b/.imgspec/install.sh
@@ -7,13 +7,11 @@ set -x
 # Define some useful directories
 imgspec_dir=$( cd "$(dirname "$0")" ; pwd -P )
 specun_dir=$(dirname ${imgspec_dir})
-cur_dir=$(pwd -P)
 
 # Install Julia and then install Julia dependencies
-conda install -y -c conda-forge julia=1.7
-cd $specun_dir
+conda create -n spectral-unmixing -y -c conda-forge julia=1.7 python=3.9
+source activate spectral-unmixing
+pushd $specun_dir
 julia -e 'using Pkg; Pkg.activate("."); Pkg.add(path="https://github.com/kmsquire/ArgParse2.jl"); Pkg.instantiate()'
 export JULIA_PROJECT=$specun_dir
-
-# Return to original directory
-cd $cur_dir
+popd

From 5b2c4e3fb1f0ac7b906693284ba7f19980dcecd5 Mon Sep 17 00:00:00 2001
From: Winston Olson-Duvall <winston.olson-duvall@jpl.nasa.gov>
Date: Fri, 1 Apr 2022 10:37:33 -0700
Subject: [PATCH 12/13] Add support for more args: n_cores, refl_nodata,
 refl_scale, and normalization

---
 .imgspec/algorithm_config.yaml | 14 ++++++++++++++
 .imgspec/imgspec_run.sh        | 27 ++++++++++++++++++++++++++-
 2 files changed, 40 insertions(+), 1 deletion(-)

diff --git a/.imgspec/algorithm_config.yaml b/.imgspec/algorithm_config.yaml
index 51bc9e7..51299c4 100644
--- a/.imgspec/algorithm_config.yaml
+++ b/.imgspec/algorithm_config.yaml
@@ -25,3 +25,17 @@ inputs:
   - name: endmember_column
     type: positional
     default: "class"
+  - name: n_cores
+    type: positional
+    default: "1"
+  - name: refl_nodata
+    type: positional
+    default: "None"
+  - name: refl_scale
+    type: positional
+    default: "None"
+  - name: normalization
+    type: positional
+    default: "None"
+
+
diff --git a/.imgspec/imgspec_run.sh b/.imgspec/imgspec_run.sh
index 1230243..61a9193 100755
--- a/.imgspec/imgspec_run.sh
+++ b/.imgspec/imgspec_run.sh
@@ -10,6 +10,11 @@
 #
 # $1: URL of endmember library
 # $2: Column name from endmember library that describes the library classes (default is "class")
+# $3: Number of cores to use (default is "1")
+# $4: Nodata value expected in input reflectance data (default is "None" - will use the repo's default)
+# $5: Scale image data (divide it by) this amount (default is "None" - will use the repo's default)
+# $6: Flag to indicate the scaling type. Options = [none, brightness, specific wavelength] (default is "None" - will
+#     use the repo's default)
 #
 # In addition to the positional arguments, this script expects a downloaded reflectance granule to be present in a
 # folder called "input".
@@ -53,6 +58,26 @@ output_base_path="output/$output_base"
 echo "Output base path: $output_base_path"
 
 # Build command and execute
-cmd="julia $unmix_exe $rfl_path $endmember_library_path $2 $output_base_path"
+cmd="julia"
+
+# Add number of cores
+if [[ $3 != "1" ]]; then
+    cmd="$cmd -p $3"
+fi
+
+# Add the required args (and assume mode is sma for now)
+cmd="$cmd $unmix_exe $rfl_path $endmember_library_path $2 $output_base_path --mode=sma"
+
+# Add the optional args
+if [[ $4 != "None" ]]; then
+    cmd="$cmd --refl_nodata=$4"
+fi
+if [[ $5 != "None" ]]; then
+    cmd="$cmd --refl_scale=$5"
+fi
+if [[ $6 != "None" ]]; then
+    cmd="$cmd --normalization=$6"
+fi
+
 echo "Executing command: $cmd"
 $cmd

From 0cc248a678c84d43ea87ac92da135c52f571cb61 Mon Sep 17 00:00:00 2001
From: Winston Olson-Duvall <winston.olson-duvall@jpl.nasa.gov>
Date: Thu, 21 Apr 2022 08:59:38 -0700
Subject: [PATCH 13/13] Use version 0.1.0 for imgspec.

---
 .imgspec/algorithm_config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.imgspec/algorithm_config.yaml b/.imgspec/algorithm_config.yaml
index 51299c4..93c6c5a 100644
--- a/.imgspec/algorithm_config.yaml
+++ b/.imgspec/algorithm_config.yaml
@@ -1,7 +1,7 @@
 # DO NOT DELETE
 # THIS CONFIG IS AUTO-GENERATED BY ADE UI
 algo_name: SpectralUnmixing
-version: imgspec
+version: 0.1.0
 environment: ubuntu
 repository_url: https://github.com/emit-sds/SpectralUnmixing.git
 docker_url: registry.imgspec.org/root/ade_base_images/vanilla:1.0